Megakaryocyte-specific knockout of the Mir-99b/let7e/125a cluster lowers platelet count without altering platelet function.

The purpose of this research was to assess the effects of a microRNA (miRNA) cluster on platelet production. Human chromosome 19q13.41 harbors an evolutionarily conserved cluster of three miRNA genes (MIR99B, MIRLET7E, MIR125A) within 727 base-pairs.

Evaluation of solid tumor response to sequential treatment cycles via a new computational hybrid approach.

The development of an in silico approach that evaluates and identifies appropriate treatment protocols for individuals could help grow personalized treatment and increase cancer patient lifespans. With this motivation, the present study introduces a novel approach for sequential treatment cycles based on simultaneously examining drug delivery, tumor growth, and chemotherapy efficacy. This model incorporates the physical conditions of tumor geometry, including tumor, capillary network, and normal tissue assuming real circumstances, as well as the intravascular and interstitial fluid flow, drug concentration, chemotherapy efficacy, and tumor recurrence.

MicroRNA Isoforms Contribution to Melanoma Pathogenesis.

Cutaneous melanoma (CM) is the most lethal tumor among skin cancers, and its incidence is constantly increasing. A deeper understanding of the molecular processes guiding melanoma pathogenesis could improve diagnosis, treatment and prognosis. MicroRNAs play a key role in melanoma biology.

Effects of hypoxia and nanocarrier size on pH-responsive nano-delivery system to solid tumors.

One of the special features of solid tumors is the acidity of the tumor microenvironment, which is mainly due to the presence of hypoxic regions. Therefore, pH-responsive drug delivery systems have recently been highly welcomed. In the present study, a comprehensive mathematical model is presented based on extravascular drug release paradigm.

A comprehensive map of alternative polyadenylation in African American and European American lung cancer patients.

Deciphering the post-transcriptional mechanisms (PTM) regulating gene expression is critical to understand the dynamics underlying transcriptomic regulation in cancer. Alternative polyadenylation (APA)-regulation of mRNA 3'UTR length by alternating poly(A) site usage-is a key PTM mechanism whose comprehensive analysis in cancer remains an important open challenge. Here we use a method and analysis pipeline that sequences 3'end-enriched RNA directly to overcome the saturation limitation of traditional 5'-3' based sequencing.

Lower extremity energy absorption strategies at different phases during single and double-leg landings with knee valgus in pubertal female athletes.

Dynamic knee valgus (DKV) malalignment affects the biomechanical characteristic during sports activities. This cross-sectional study was conducted to evaluate mechanical energy absorption (MEA) strategies at initial contact (IC) and total landing (TL) phases during single-leg landing (SLL), and double-leg landing (DLL). Twenty-eight female athletes with DKV (age 10-14) were invited.

RNase κ promotes robust piRNA production by generating 2',3'-cyclic phosphate-containing precursors.

In animal germlines, PIWI proteins and the associated PIWI-interacting RNAs (piRNAs) protect genome integrity by silencing transposons. Here we report the extensive sequence and quantitative correlations between 2',3'-cyclic phosphate-containing RNAs (cP-RNAs), identified using cP-RNA-seq, and piRNAs in the Bombyx germ cell line and mouse testes. The cP-RNAs containing 5'-phosphate (P-cP-RNAs) identified by P-cP-RNA-seq harbor highly consistent 5'-end positions as the piRNAs and are loaded onto PIWI protein, suggesting their direct utilization as piRNA precursors.

Efficacy of Location-Based Features for Survival Prediction of Patients With Glioblastoma Depending on Resection Status.

Cancer stands out as one of the fatal diseases people are facing all the time. Each year, a countless number of people die because of the late diagnosis of cancer or wrong treatments. Glioma, one of the most common primary brain tumors, has different aggressiveness and sub-regions, which can affect the risk of disease.

The Short and the Long of it: Timing of Mortality for Older Adults in a State Trauma System.

Background: The impact of injury extends beyond the hospital stay, but trauma center performance metrics typically focus on in-hospital mortality. We compared risk adjusted rates of in-hospital and long-term mortality among Pennsylvania trauma centers. We hypothesized that centers with low rates of in-hospital mortality would also have low rates of long-term mortality.

Mathematical simulation and prediction of tumor volume using RBF artificial neural network at different circumstances in the tumor microenvironment.

Uncontrolled proliferation of cells in a tissue caused by genetic mutations inside a cell is referred to as a tumor. A tumor which grows rapidly encounters a barrier when it grows to a certain size in presence of preexisting vasculature. This is the time when it has to find a way to go on the growth.

Multiscale modeling of tumor growth and angiogenesis: Evaluation of tumor-targeted therapy.

The dynamics of tumor growth and associated events cover multiple time and spatial scales, generally including extracellular, cellular and intracellular modifications. The main goal of this study is to model the biological and physical behavior of tumor evolution in presence of normal healthy tissue, considering a variety of events involved in the process. These include hyper and hypoactivation of signaling pathways during tumor growth, vessels' growth, intratumoral vascularization and competition of cancer cells with healthy host tissue.

Numerical Methods in Studies of Liquid Crystal Elastomers.

Liquid crystal elastomers (LCEs) are a type of material with specific features of polymers and of liquid crystals. They exhibit interesting behaviors, i.e.

Unraveling the role of microRNA/isomiR network in multiple primary melanoma pathogenesis.

Malignant cutaneous melanoma (CM) is a potentially lethal form of skin cancer whose worldwide incidence has been constantly increasing over the past decades. During their lifetime, about 8% of CM patients will develop multiple primary melanomas (MPMs), usually at a young age and within 3 years from the first tumor/diagnosis. With the aim of improving our knowledge on MPM biology and pathogenesis, we explored the miRNome of 24 single and multiple primary melanomas, including multiple tumors from the same patient, using a small RNA-sequencing approach.

Microfluidic platform for synthesis and optimization of chitosan-coated magnetic nanoparticles in cisplatin delivery.

In this study, magnetic core/chitosan shell Nanoparticles (NPs) containing cisplatin were synthesized via cisplatin complexation with tripolyphosphate as the chitosan crosslinker using two different procedures: a conventional batch flow method and a microfluidic approach. An integrated microfluidic device composed of three stages was developed to provide precise and highly controllable mixing. The comparison of the results revealed that NPs synthesized in microchannels were monodisperse 104 ± 14.

In vitro production and multiplex quantification of 2',3'-cyclic phosphate-containing 5'-tRNA half molecules.

RNA cleavages by many ribonucleases generate RNA molecules that contain a 2',3'-cyclic phosphate (cP) at their 3'-termini, and many cP-containing RNAs (cP-RNAs) are expressed as functional molecules in cells and tissues. 5'-tRNA half molecules are representative examples of functional cP-RNAs, playing important roles in various biological processes. We here show in vitro production of cP-containing 5'-tRNA half molecules that is able to prepare abundant synthetic cP-RNAs enough for functional analyses.

The transcriptional trajectories of pluripotency and differentiation comprise genes with antithetical architecture and repetitive-element content.

Background: Extensive molecular differences exist between proliferative and differentiated cells. Here, we conduct a meta-analysis of publicly available transcriptomic datasets from preimplantation and differentiation stages examining the architectural properties and content of genes whose abundance changes significantly across developmental time points.

Results: Analysis of preimplantation embryos from human and mouse showed that short genes whose introns are enriched in Alu (human) and B (mouse) elements, respectively, have higher abundance in the blastocyst compared to the zygote.

STATegra: Multi-Omics Data Integration - A Conceptual Scheme With a Bioinformatics Pipeline.

Technologies for profiling samples using different omics platforms have been at the forefront since the human genome project. Large-scale multi-omics data hold the promise of deciphering different regulatory layers. Yet, while there is a myriad of bioinformatics tools, each multi-omics analysis appears to start from scratch with an arbitrary decision over which tools to use and how to combine them.

Machine Learning Approaches Identify Genes Containing Spatial Information From Single-Cell Transcriptomics Data.

The development of single-cell sequencing technologies has allowed researchers to gain important new knowledge about the expression profile of genes in thousands of individual cells of a model organism or tissue. A common disadvantage of this technology is the loss of the three-dimensional (3-D) structure of the cells. Consequently, the Dialogue on Reverse Engineering Assessment and Methods (DREAM) organized the Single-Cell Transcriptomics Challenge, in which we participated, with the aim to address the following two problems: (a) to identify the top 60, 40, and 20 genes of the embryo that contain the most spatial information and (b) to reconstruct the 3-D arrangement of the embryo using information from those genes.

A neuro evolutionary algorithm for patient calibrated prediction of survival in Glioblastoma patients.

Background And Objectives: Glioblastoma multiforme (GBM) is the most common and malignant type of primary brain tumors. Radiation therapy (RT) plus concomitant and adjuvant Temozolomide (TMZ) constitute standard treatment of GBM. Existing models for GBM growth do not consider the effect of different schedules on tumor growth and patient survival.

IsoMiRmap: fast, deterministic and exhaustive mining of isomiRs from short RNA-seq datasets.

Motivation: MicroRNA (miRNA) precursor arms give rise to multiple isoforms simultaneously called 'isomiRs.' IsomiRs from the same arm typically differ by a few nucleotides at either their 5' or 3' termini or both. In humans, the identities and abundances of isomiRs depend on a person's sex and genetic ancestry as well as on tissue type, tissue state and disease type/subtype.

Evaluation of inverse methods for estimation of mechanical parameters in solid tumors.

To treat cancer, knowledge of mechanical parameters can be essential. This study proposes a new approach for estimating hydraulic conductivity (k) and hydraulic conductivity ratio (α) of a living tissue, based on inverse methods, allowing tissue parameter estimation using only a limited set of measurements. First, two population-based algorithms (Levenberg-Marquardt (LM) method and conjugate gradient (CG) method) and two gradient-based algorithms (genetic algorithm (GA) and particle swarm optimization (PSO) algorithm) are considered, and a comparative study between these different inverse methods is performed to determine which methods have a good performance in terms of convergence rate and stability.

Modulation of Aub-TDRD interactions elucidates piRNA amplification and germplasm formation.

Aub guided by piRNAs ensures genome integrity by cleaving retrotransposons, and genome propagation by trapping mRNAs to form the germplasm that instructs germ cell formation. Arginines at the N-terminus of Aub (Aub-NTRs) interact with Tudor and other Tudor domain-containing proteins (TDRDs). Aub-TDRD interactions suppress active retrotransposons via piRNA amplification and form germplasm via generation of Aub-Tudor ribonucleoproteins.

Biodegradable Nanoparticle for Cornea Drug Delivery: Focus Review.

During recent decades, researchers all around the world have focused on the characteristic pros and cons of the different drug delivery systems for cornea tissue change for sense organs. The delivery of various drugs for cornea tissue is one of the most attractive and challenging activities for researchers in biomaterials, pharmacology, and ophthalmology. This method is so important for cornea wound healing because of the controllable release rate and enhancement in drug bioavailability.

Infection-induced 5'-half molecules of tRNAHisGUG activate Toll-like receptor 7.

Toll-like receptors (TLRs) play a crucial role in the innate immune response. Although endosomal TLR7 recognizes single-stranded RNAs, their endogenous RNA ligands have not been fully explored. Here, we report 5'-tRNA half molecules as abundant activators of TLR7.